CometModification Struct Reference

Helper struct to represent a Comet variable modification entry. More...

#include <OpenMS/ANALYSIS/ID/CometModification.h>

Collaboration diagram for CometModification:

Public Member Functions
	CometModification ()=default
	Default constructor.
	CometModification (const ResidueModification *mod, int binary_grp, int max_mods)
	Constructor from ResidueModification.
bool	isMergeableWith (const CometModification &other) const
	Check if this modification can be merged with another.
void	merge (const CometModification &other)
	Merge another modification into this one.
String	toCometString (Size index) const
	Generate the Comet param file line format for the given 1-based index.

Static Public Member Functions
static std::vector< CometModification >	mergeModifications (const std::vector< CometModification > &mods)
	Merge a vector of CometModifications, combining compatible entries.

Public Attributes
double	mass {0.0}
	Modification mass difference.
String	residues
	Residue(s) this modification applies to (e.g., "K", "KR", "n", "nKR")
int	binary_group {0}
	Binary modification group (for SILAC etc.)
int	max_mods_per_peptide {5}
	Maximum number of this modification per peptide.
int	term_distance {-1}
	Terminal distance (-1 = no constraint, 0 = terminal only)
int	nc_term {0}
	Terminal specificity: 0=protein N-term, 1=protein C-term, 2=peptide N-term, 3=peptide C-term.
bool	required {false}
	Whether this modification is required.

Static Public Attributes
static constexpr double	MASS_TOLERANCE = 1e-6
	Mass tolerance for comparing modification masses.

Detailed Description

Helper struct to represent a Comet variable modification entry.

This struct facilitates merging of modifications with the same mass and compatible term specificity. Comet supports specifying multiple residues in a single modification entry (e.g., "KR" for lysine and arginine), which significantly improves search performance.

Merging rules based on Comet's internal logic and documentation:

• Modifications with the same mass and binary group can be merged
• Amino acid mods can merge with each other (e.g., "K" + "R" -> "KR")
• Peptide N-term and amino acids can be merged (e.g., "n" + "RST" -> "nRST")
• Peptide C-term and amino acids can be merged (e.g., "c" + "KR" -> "cKR")
• Protein terminal mods (nc_term 0 or 1) must remain separate
• Peptide N-term and C-term cannot merge with each other

When terminal and amino acid mods merge, term_distance becomes -1 and nc_term becomes 0, because the terminal specificity is encoded by 'n'/'c' in the residue string (as per Comet documentation: e.g., "42.010565 nK 0 3 -1 0 0 0.0").

Constructor & Destructor Documentation

CometModification() [1/2]

CometModification ( )

default

Default constructor.

CometModification() [2/2]

CometModification	(	const ResidueModification *	mod,
		int	binary_grp,
		int	max_mods
	)

Constructor from ResidueModification.

Member Function Documentation

isMergeableWith()

bool isMergeableWith

(

const CometModification &

other

)

const

Check if this modification can be merged with another.

merge()

void merge

(

const CometModification &

other

)

Merge another modification into this one.

mergeModifications()

static std::vector< CometModification > mergeModifications ( const std::vector< CometModification > &  mods )

static

Merge a vector of CometModifications, combining compatible entries.

toCometString()

String toCometString

(

Size

index

)

const

Generate the Comet param file line format for the given 1-based index.

Member Data Documentation

binary_group

int binary_group {0}

Binary modification group (for SILAC etc.)

mass

double mass {0.0}

Modification mass difference.

MASS_TOLERANCE

constexpr double MASS_TOLERANCE = 1e-6

staticconstexpr

Mass tolerance for comparing modification masses.

max_mods_per_peptide

int max_mods_per_peptide {5}

Maximum number of this modification per peptide.

nc_term

int nc_term {0}

Terminal specificity: 0=protein N-term, 1=protein C-term, 2=peptide N-term, 3=peptide C-term.

required

bool required {false}

Whether this modification is required.

residues

String residues

Residue(s) this modification applies to (e.g., "K", "KR", "n", "nKR")

term_distance

int term_distance {-1}

Terminal distance (-1 = no constraint, 0 = terminal only)